Ben Stokes top scored with 42 and Adil Rashid finished unbeaten on 35, as Australia all-rounder Mitchell Marsh collected an impressive four for 27 while John Hastings claimed three for 21.
Morgan, who had scored one run and faced six balls prior to the incident, was struck on the helmet by a short ball just below his right ear from left-arm fast bowler Mitchell Starc in the seventh over.
Australia's players immediately surrounded Dublin-born Morgan after he sustained the blow and following treatment by the England medical staff on the pitch the 29-year-old climbed to his feet and made his way back to the dressing room.
Australia opening batsman Phillip Hughes died in November last year after he was struck on the neck by a delivery in a first-class match in Sydney.
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Nottinghamshire batsman James Taylor has taken over captaincy duties for the rest of the match in Morgan's absence.
And, having won the toss and then watched his side compile 300-8 then bowl Australia out for 207 at the same venue in the third ODI last week, skipper Morgan again elected to bat when he called correctly.
However, Australia's pace attack bowled tight lines and aggressively as they took wickets at crucial times to bowl England out in 33 overs.
England lost opener Jason Roy (4) lbw to Starc early on, although replays showed the ball had been missing the stumps, but the opener took too long to decide whether to review the decision.
Stokes added a degree of respectability to the score with a 51-ball 42 which included six fours and one six while Rashid boosted the total in a last-wicket stand of 32 with England debutante Reece Topley.
However, their partnership was brought to halt when the stoic Topley was trapped plumb lbw by Ashton Agar for six.